PT  - JOURNAL ARTICLE
AU  - Miguel D. Fernández-de-Bobadilla
AU  - Alba Talavera-Rodríguez
AU  - Lucía Chacón
AU  - Fernando Baquero
AU  - Teresa M. Coque
AU  - Val F. Lanza
TI  - PATO: Pangenome Analysis Toolkit
AID  - 10.1101/2021.01.30.428878
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.01.30.428878
4099  - http://biorxiv.org/content/early/2021/02/01/2021.01.30.428878.short
4100  - http://biorxiv.org/content/early/2021/02/01/2021.01.30.428878.full
AB  - Motivation Comparative genomics is a growing field but one that will be eventually overtaken by sample size studies and the increase of available genomes in public databases. We present the Pangenome Analysis Toolkit (PATO) designed to simultaneously analyze thousands of genomes using a desktop computer. The tool performs common tasks of pangenome analysis such as core-genome definition and accessory genome properties and includes new features that help characterize population structure, annotate pathogenic features and create gene sharedness networks. PATO has been developed in R to integrate with the large set of tools available for genetic, phylogenetic and statistical analysis in this environment.Results PATO can perform the most demanding bioinformatic analyses in minutes with an accuracy comparable to state-of-the-art software but 20–30x times faster. PATO also integrates all the necessary functions for the complete analysis of the most common objectives in microbiology studies. Lastly, PATO includes the necessary tools for visualizing the results and can be integrated with other analytical packages available in R.Availability The source code for PATO is freely available at https://github.com/irycisBioinfo/PATO under the GPLv3 license.Contact val.fernandez{at}salud.madrid.orgSupplementary information Supplementary data are available at Bioinformatics onlineCompeting Interest StatementThe authors have declared no competing interest.